VMD-L Mailing List
From: Xu (fangxu_at_levdec.engr.ccny.cuny.edu)
Date: Sat Jun 24 2006 - 20:51:27 CDT
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Hello,
I want to visualize a polymer chain described by a set of bead-rod. In
order to introduce the bond information, I wrote a fake psf file as
following:
PSF
11 !NATOM
1 U 1 0 C C 0.00000 0 0
2 U 1 0 C C 0.00000 0 0
3 U 1 0 C C 0.00000 0 0
4 U 1 0 C C 0.00000 0 0
5 U 1 0 C C 0.00000 0 0
6 U 1 0 C C 0.00000 0 0
7 U 1 0 C C 0.00000 0 0
8 U 1 0 C C 0.000000 0 0
9 U 1 0 C C 0.00000 0 0
10 U 1 0 C C 0.00000 0 0
11 U 1 0 C C 0.00000 0 0
10 !NBOND: bonds
1 2 2 3 3 4 4 5
5 6 6 7 7 8 8 9
9 10 10 11
However, VMD can not read the bond information and gives the error
information:
ERROR) Error reading bond information.
Info) Analyzing structure ...
Info) Atoms: 11
Info) Bonds: 0
Info) Residues: 11
Info) Waters: 0
Info) Segments: 2
Info) Fragments: 11 Protein: 0 Nucleic: 0
Why is that? Is there any constraint on defining bonds? Any suggestions?
Many thanks.
Fang
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